Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1000211 | ENA |
REPOSITORIES: ENA
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Project description:This Phase Ib trial studies the side effects and best dose of LB-100 and azenosertib for the treatment of patients with metastatic colorectal cancer. Azenosertib blocks a protein that is involved in the repair of damaged DNA, this protein is called WEE1. Inhibiting WEE1 drives cancer cells into a state of cell division without repair of the damaged DNA, resulting in cell death. LB-100 has been shown to make anticancer drugs work better at killing cancer. LB-100 blocks a protein called PP2A. Blocking this protein increases the stress signals for the tumor cells that express PP2A. Research has shown that azenosertib and LB-100 may enhance each others effect when treating metastatic colorectal cancer.
| 116295 | ecrin-mdr-crc
Project description:Chromatin from LNCaP-C4-2B cells was immunoprecipitated using pY88-H4 or IgG antibodies, followed by sequencing of the ChIP-DNA Examination of the distribution of pY88-H4 epigenetic marks in CRPC cell line
2016-03-29 | E-GEOD-79658 | biostudies-arrayexpress
Project description:Bisulphite sequencing enables DNA methylation analysis of every cytosine residue. We have optimized conditions for combining chromatin immunoprecipation (ChIP) with high throughput bisulphite sequencing to study the relationship between histone modifications and DNA methylation. Paired-end bisulphite sequencing of H3K27me3-ChIP DNA for LNCaP and PrEC cell lines
2012-01-18 | E-GEOD-30558 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare AR binding activity in LNCaP cells with and without knockdown of GATA2. Methods: LNCaP cells between passage number 32-34 were used for assay. Cells are transfected with GATA2 specific or nonspecific siRNA and ChIP was performed, the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks. Results: GATA2 knockdown lead to changes of AR binding activity , in most AR binding sites, AR shows decreased bindig activity. Only small percent sites show increased binding. Conclusions: Our study represents the first detailed analysis of the relationship between GATA2 and AR binding in whole genomic DNA.These results demostrate GATA2 play a critical role in AR activity in prostate cancer. LNCaP cells was used as cell model were treated with specific GATA2 siRNA.Library was sequenced using Illumina HI-seq 2500.
2014-01-21 | E-GEOD-52725 | biostudies-arrayexpress
Project description:Chromatin from LNCaP-C4-2B cells was immunoprecipitated using pY88-H4 or IgG antibodies, followed by sequencing of the ChIP-DNA
2016-03-29 | GSE79658 | GEO
Project description:To investiagate copy number differences between PrEC and LNCaP cells, each was DNA sequenced. One PrEC sample, a normal cell line. One LNCaP sample, a cancer cell line.
2012-11-30 | E-GEOD-38674 | biostudies-arrayexpress
Project description:CRPC remains AR dependent. There are multiple mechanisms for reactivation of AR including expression of constitutively active AR splices variant AR-V7 (AR3). Earlier studies suggest that though the variants regulate many of the same genes as AR, they also have unique targets. Another argument is that the variant is a “weak” AR. We have used an LNCaP cell line that expresses AR-V7 in response to doxycycline to compare DNA interactions of the two isoforms and to identify differential regulation of target genes. ChIP-exo method was used to map AR and AR-V7 interaction with DNA in LNCaP engineered cell line (LNCaP AR-V7) at single base resolution.
2021-07-07 | GSE143906 | GEO
Project description:Purpose: The dynamic chromatin accessibility was regulated by pioneer factors. The goals of this study are revealing the mechanism of GATA2 and SOX9 required for the change of nucleosome states. Methods: LNCaP cells between passage number 30-35 were used for assay. cell nucleus was extracted, digested by Tn5 transposase and ChIP was performed, the ChIP products were further used to generate library with illumina ChIP-seq kit. Hi-seq 3000 was used for sequencing and the data was analyzed by MACS2 for peaks. Results: GATA2 is associated with condensed nucleosome states and SOX9 is recruit for unwrapped the nucleosomes. Conclusions: Our study represents the first detailed nucleosome footprint of LNCap cells and mechanism underlining GATA2 and nucleosome reorganization in whole genomic DNA.
2021-12-09 | GSE182529 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE30558: Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChiP-seq) directly informs methylation status GSE34340: Bisulphite sequencing of native LNCaP and PrEC DNA [methylation array] Refer to individual Series
2012-01-18 | E-GEOD-34403 | biostudies-arrayexpress
Project description:Purpose: The dynamic nucleosome reorganization is the interplay among nucleosome and regulated by pioneer factors, which can access target DNA sequences on nucleosomes.The goals of this study are revealing the dynamic nucleosome footprint and how GATA2 is capable of resetting crowding array to primed, or accessible edge nucleosome states. Methods: LNCaP cells between passage number 30-35 were used for assay. cell nucleus was extracted, digested by MNase to Mono-nucleosome and ChIP/ChIP-exo was performed, the ChIP products were further used to generate library with illumina ChIP-seq kit. Hi-seq 3000 was used for sequencing and the data was analyzed by MACS2 for peaks. Results: GATA2 is associated with condensed nucleosome states and nucleosomes could unwrapped and be more accessible in pioneer factor GATA2 binding sites. Conclusions: Our study represents the first detailed nucleosome footprint of LNCap cells and analysis of the relationship between pioneer factor GATA2 and nucleosome reorganization in whole genomic DNA. These results demonstrated GATA2 play a critical role in an AR-independent manner in prostate cancer.
2021-04-14 | GSE148935 | GEO